We developed a pipeline to integrate independent contig assemblies and curate assembly errors using Bionano maps as an anchor. The pipeline consists of five steps: (1) conflict resolution, (2) assembly error curation, (3) contig merging, (4) hybrid assembly and contig overlap removal, and (5) manual curation and gap filling. The first four steps were automated. A gapless chromosome 3 was generated upon contig merging in the third step, and the complete assembly of chromosome 9 required manual curation. The availability of de novo assembled Bionano maps is necessary to perform conflict-cutting in step 1, contig error correction in step 2, and hybrid scaffolding in step 4 of the pipeline.